Stockfish uses the UCI protocol to communicate with a GUI. A nice overview of this protocol is available at Wikipedia.
The actual documentation is available for download at: http://download.shredderchess.com/div/uci.zip
An abridged summary of notable UCI commands follows. This is useful if you are running Stockfish from the command line.
position fen rnbqkbnr/pppppppp/8/8/8/8/PPPPPPPP/RNBQKBNR w KQkq - 0 1
This sets the position with a FEN string. As always, Wikipedia has an overview of this notation.
position startpos moves e2e4
This sets the position with moves starting from the starting position. This notation is preferred because the engine can take into account such things as the 50-move rule or threefold repetition.
This outputs the list of settings.
setoption name Hash value 1024
This sets the hash size to 1 GB.
setoption name Threads value 4
This asks Stockfish to use 4 threads when analyzing.
Asks the engine to analyze forever. Send the
command to stop analysis or press
CTRL + C to
go depth 20
Asks the engine to analyze to a specific depth.
go movetime 5000
Asks the engine to analyze for 5 seconds.